They were only able to return about 15% of the items because they could not get enough to claim them, said FBI Special Agent Tim Carpenter in a statement.
The artifacts, which are part of the "largest collection of cultural property in the history of the FBI," were discovered in 2014, the FBI said in a statement.
A tip has led the FBI's FBI team at a Waldron farm in Indiana, where thousands of artifacts from around the world and even the remains of hundreds of thousands Native Americans are stored.
Don Miller, the farm's owner, was a "retired scientist who helped build the first atomic bomb," according to the FBI. He had traveled extensively for decades and had collected more than 42,000 items at home.
"Don (Miller) would collect just about anything," FBI Special Agent Tim Carpenter said in a statement. "He gathered around every corner of the world."
"But his passion, I think, was Native American cultural property," he added.
The FBI says some of the artifacts were illegally obtained.
Before his death in 2015, Miller had agreed to give the FBI artifacts that he had acquired in violation of "federal law and state laws and international treaties," officials said.
"He cooperated with us throughout the investigation," said Carpenter, "and he wanted us to recover these items and return them to their rightful owners, and that the ancestors of the Native Americans should be properly reentered." .
For nearly five years, the FBI has worked with archaeologists, anthropologists, tribal experts and foreign governments to manage and return human remains. Holly Cusack-McVeigh, Associate Professor of Anthropology and Museum Studies at Indiana University at Purdue University in Indianapolis, works with her students to prepare and prepare papers for dispatch.
"We make sure that nothing is simply thrown in checked luggage and thrown into the belly of a plane – everything is treated with the utmost care," said Cusack-McVeigh.
But it's not easy to determine where everything should be returned.
"There is not a single expert able to tell us everything we need to know about all this material," Carpenter said.
Authorities contacted hundreds of Amerindian tribes and informed UN members of artifacts recovered in the hope of identifying them. They also gave them access to a private website where they can review and claim the items.
And yet, the future of thousands of items in a climate-controlled warehouse outside of Indianapolis is still unclear.
"Our ultimate goal is to repatriate each of these pieces, at least the ones we can determine were obtained incorrectly or illegally," Carpenter said. "But we need the help of the public and the universities, and we need the help of our foreign partners to do it."
The FBI is urging Native American tribes and nations around the world to determine if they can claim the artifacts, contact the agency and submit a request to the address email@example.com.
CNN's Carma Hassan contributed to this report.